Abstract 5934: Tracking T cell clonal dynamics across time and space in metastatic colorectal cancer
Authors: Ann-Marie Baker, Alison Berner, Tahel Ronel, Nick Trahearn, Barbara Bravi, John Bridgewater, Benny Chain, Trevor A. Graham
Journal: Cancer Research (2023)

Abstract Here we tracked T cell dynamics in 15 metastatic colorectal cancer (mCRC) patients who had multiple resections (median: 3, range: 2-7) over a period of &amp;gt;7 years (median: 10 years, range: 7-16 years), using a novel T cell receptor sequencing (TCRseq) method. These samples had been previously characterized for DNA and methylation alterations and gene expression, enabling an integrated analysis to determine potential cellular and molecular drivers and consequences of immune dynamics. This multi-region, multi-timepoint dataset presents a unique opportunity to study the co-evolution of mCRC and the T cell response over time, across metastatic sites and in response to therapy. T cell antigen specificity is defined by the TCR - a highly diverse sequence that enables tracking of specific T cell expansions across time and space. TCRseq quantifies the abundance of T cell clones and maps the dynamics of the TCR repertoire, however little is known about how these are altered in different metastatic sites, and post-chemotherapy. We developed and validated a new FFPE-compatible TCRseq method and sequenced 216 longitudinal samples representing the mCRC cohort described above. We detected a median of 348 unique TCRs per sample (range 69-9700), and revealed high levels of intra-tumor spatial heterogeneity. No significant difference was detected in the number of T cell clones or the TCR clonality between primary tumors (n=40), lung metastases (n=30) and liver metastases (n=50). Furthermore, these were not significantly different between tumor regions (n=139) and surrounding stroma (n=38). We found that compared to chemo-naïve tumors (n=36), those that had been exposed to recent chemotherapy (n=41) had a significant increase in both the number of unique T cell clones and Simpson’s evenness, likely reflecting a broad T cell response to DNA-damaging agents. After more than a year had passed without chemotherapy (n=64) these returned to pre-chemotherapy levels. In most cases the 10 most abundant TCR sequences in the primary tumor represented 15-40% of the total repertoire. We tracked these expanded clones through metastases, identifying ubiquitous clones which persisted across metastatic sites and through therapy. We found other expanded clones which were no longer present in metastases lesions, although some of these were found to expand again in later metastases. Finally, we examined correlations with tumor genomics, finding evidence in some patients that the TCR repertoire tracks closely with tumor clones even through metastasis and chemotherapy. In summary, this project represents the first comprehensive analysis of T cell dynamics through colorectal cancer metastasis, highlighting the changing T cell landscape post-chemotherapy and correlating the TCR repertoire with tumor genomics. Our results could have important clinical implications for mCRC immunotherapy and the design of personalized T cell-based therapy. Citation Format: Ann-Marie Baker, Alison Berner, Tahel Ronel, Nick Trahearn, Barbara Bravi, John Bridgewater, Benny Chain, Trevor A. Graham. Tracking T cell clonal dynamics across time and space in metastatic colorectal cancer. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5934.